Predicting pseudoknotted structures across two RNA sequences.
Bioinformatics
; 28(23): 3058-65, 2012 Dec 01.
Article
em En
| MEDLINE
| ID: mdl-23044552
ABSTRACT
MOTIVATION Laboratory RNA structure determination is demanding and costly and thus, computational structure prediction is an important task. Single sequence methods for RNA secondary structure prediction are limited by the accuracy of the underlying folding model, if a structure is supported by a family of evolutionarily related sequences, one can be more confident that the prediction is accurate. RNA pseudoknots are functional elements, which have highly conserved structures. However, few comparative structure prediction methods can handle pseudoknots due to the computational complexity. RESULTS:
A comparative pseudoknot prediction method called DotKnot-PW is introduced based on structural comparison of secondary structure elements and H-type pseudoknot candidates. DotKnot-PW outperforms other methods from the literature on a hand-curated test set of RNA structures with experimental support.AVAILABILITY:
DotKnot-PW and the RNA structure test set are available at the web site http//dotknot.csse.uwa.edu.au/pw. CONTACT janaspe@csse.uwa.edu.au SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Software
/
RNA
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Análise de Sequência de RNA
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Dobramento de RNA
Tipo de estudo:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Ano de publicação:
2012
Tipo de documento:
Article